<scp>HLA</scp>‐<scp>DQA</scp>1 and <scp>HLA</scp>‐<scp>DQB</scp>1 allele diversity and its extended haplotypes in Madeira Island (Portugal)

Spínola, Hélder; Lemos, Andreia; Couto, Ana Rita; Parreira, Bárbara; Soares, M.J.; Dutra, Inês; Bruges-Armas, Jácome; Brehm, António

doi:10.1111/iji.12300

Cited by 3 publications

(4 citation statements)

References 13 publications

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“…The HLA genes encoded major histocompatibility complex ( MHC ) class I proteins in the context of specific cell surfaces (Valenzuela-Ponce et al, 2018), involving HLA-A, HLA-B, HLADRB1, HLA-DQA1 , and HLA-DQB1 (Emerson et al, 2017). HLA played a major role in the control of the immune response and its associations with a wide variety of immunological and infectious disorders, such as type I diabetes, multiple sclerosis, rheumatoid arthritis, Grave's disease, ankylosing spondylitis, and systemic lupus erythematosus (Spínola et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids

Cao

et al. 2019

Front. Genet.

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Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds.

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Section: Resultsmentioning

confidence: 99%

Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids

Cao

et al. 2019

Front. Genet.

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“…All subjects were high‐resolution genotyped for HLA‐DRB1, HLA‐DQA1 and HLA‐DQB1 by polymerase chain reaction using commercial sequence‐specific primers (PCR‐SSP) (Olerup) (Olerup & Zetterquist, ) and sequence‐specific oligonucleotide probes (PCR‐SSO) (Luminex) kits (Cesbron‐Gautier et al., ). One hundred and sixty‐four healthy unrelated males previously typed for HLA‐DRB1, HLA‐DQA1 and HLA‐DQB1 (Spínola et al., , ) were used as a population‐based control sample. Only individuals with parents and grandparents born and living in the island were included in the study so we avoided more recent introductions.…”

Section: Methodsmentioning

confidence: 99%

Human leucocyte antigens class II allele and haplotype association with Type 1 Diabetes in Madeira Island (Portugal)

Spínola

Lemos

Couto

et al. 2017

Int J Immunogenetics

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This study confirms for Madeira Island (Portugal) population the Type 1 Diabetes (T1D) susceptible and protective Human leucocyte antigens (HLA) markers previously reported in other populations and adds some local specificities. Among the strongest T1D HLA associations, stands out, as susceptible, the alleles DRB1*04:05 (OR = 7.3), DQB1*03:02 (OR = 6.1) and DQA1*03:03 (OR = 4.5), as well as the haplotypes DRB1*04:05-DQA1*03:03-DQB1*03:02 (OR = 100.9) and DRB1*04:04-DQA1*03:01-DQB1*03:02 (OR = 22.1), and DQB1*06:02 (OR = 0.07) and DRB1*15:01-DQA1*01:02-DQB1*06:02 (OR = 0.04) as protective. HLA-DQA1 positive for Arginine at position 52 (Arg52) (OR = 15.2) and HLA-DQB1 negative for Aspartic acid at the position 57 (Asp57) (OR = 9.0) alleles appear to be important genetic markers for T1D susceptibility, with higher odds ratio values than any single allele and than most of the haplotypes. Genotypes generated by the association of markers Arg52 DQA1 positive and Asp57 DQB1 negative increase T1D susceptibility much more than one would expected by a simple additive effect of those markers separately (OR = 26.9). This study also confirms an increased risk for DRB1*04/DRB1*03 heterozygote genotypes (OR = 16.8) and also a DRB1*04-DQA1*03:01-DQB1*03:02 haplotype susceptibility dependent on the DRB1*04 allele (DRB1*04:01, OR = 7.9; DRB1*04:02, OR = 3.2; DRB1*04:04, OR = 22.1).

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“…The HLA polymorphism has been deeply studied across populations, however, most studies focused on HLA‐A, HLA‐B , and HLA‐DRB1 as their implication for transplantation outcome has been known for longer. The diversity of non‐classical HLA genes and of genes that encode the alpha chain of the classical class II molecules is poorly known across populations, despite the growing evidence of their impact in disease and transplantation . Even scarcer are the studies that describe the classical and non‐classical genes in a single population sample.…”

Section: Introductionmentioning

confidence: 99%

“…The diversity of non-classical HLA genes and of genes that encode the alpha chain of the classical class II molecules is poorly known across populations, despite the growing evidence of their impact in disease and transplantation. [20][21][22][23][24][25][26][27][28] Even scarcer are the studies that describe the classical and non-classical genes in a single population sample.…”

Section: Introductionmentioning

confidence: 99%

High‐resolution characterization of 12 classical and non‐classical HLA loci in Southern Brazilians

Castro

Issler

Gelmini

et al. 2019

HLA

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The human leukocyte antigen (HLA) are the most polymorphic genes in the human genome. Because of their importance for antigen recognition, HLA molecules play a central role in host defense and graft rejection upon transplantation. The aim of this study was to characterize allelic diversity of the classical HLA genes HLA‐A, ‐B, ‐C, ‐DRA, ‐DRB1, ‐DQA1, ‐DQB1, ‐DPA1, ‐DPB1, and the non‐classical class I genes HLA‐E, ‐F and ‐G at high‐resolution for a population of predominantly European ancestry from Curitiba, Brazil. Genotyping of 108 individuals was performed by next‐generation sequencing on the MiSeq platform and also by Sanger sequencing. The genotype distributions of all loci were in accordance with Hardy‐Weinberg equilibrium (P > 0.05) and a total of 202 HLA variants at second field resolution were observed for the 12 loci. The strongest linkage disequilibrium (r2 = 1.0, P < 10−5) was observed for the following pairs of alleles: HLA‐B*42:01:01 ~ HLA‐DRB1*03:02:01; HLA‐B*14:02:01 ~ HLA‐C*08:02:01; B*42:01:01 ~ HLA‐C*17:01:01; HLA‐DRB1*03:01:01 ~ HLA‐DQB1*02:01:01 ~ DRB1*03:01:01 ~ HLA‐DQB1*02:01:01; DRB1*13:01:01~ HLA‐DQB1*06:03:01 and HLA‐DRB1*09:01:02 ~ HLA‐DQA1*03:02. This is the first study to characterize all 12 HLA genes at high resolution in a single population. On the basis of the allelic frequencies of worldwide populations and principal component analysis, we confirmed the similarity of the study population to European and other Euro‐descendant populations.

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HLA‐DQA1 and HLA‐DQB1 allele diversity and its extended haplotypes in Madeira Island (Portugal)

Cited by 3 publications

References 13 publications

Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids

Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids

Human leucocyte antigens class II allele and haplotype association with Type 1 Diabetes in Madeira Island (Portugal)

High‐resolution characterization of 12 classical and non‐classical HLA loci in Southern Brazilians

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